Home LiteratureArticle Details
PMID: 14576293 Published · ppublish English Journal Article Review

Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities.

Nucleic acids research ·Vol. 31 ·No. 21 ·2003-11-01 ·Pages 6064-78

Uil TG, Haisma HJ, Rots MG

Abstract

Designer molecules that can specifically target pre-determined DNA sequences provide a means to modulate endogenous gene function. Different classes of sequence-specific DNA-binding agents have been developed, including triplex-forming molecules, synthetic polyamides and designer zinc finger proteins. These different types of designer molecules with their different principles of engineered sequence specificity are reviewed in this paper. Furthermore, we explore and discuss the potential of these molecules as therapeutic modulators of endogenous gene function, focusing on modulation by stable gene modification and by regulation of gene transcription.

MeSH Terms
Animals DNA/chemistry,genetics,metabolism DNA-Binding Proteins/metabolism Gene Expression Regulation Humans Nylons/metabolism Substrate Specificity Transcription Factors/metabolism
Chemicals
DNA-Binding Proteins Nylons Transcription Factors triplex DNA DNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Uil Taco G
Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.
Haisma Hidde J
Rots Marianne G
References (181)
181 references, click to expand
  1. Blocking transcription through a nucleosome with synthetic DNA ligands.
    J Mol Biol. 2002 Aug 9;321(2):249-63 PMID: 12144782
  2. Cellular uptake of N-methylpyrrole/N-methylimidazole polyamide-dye conjugates.
    Bioorg Med Chem. 2002 Oct;10(10):3313-8 PMID: 12150878
  3. DNA crosslinking and biological activity of a hairpin polyamide-chlorambucil conjugate.
    Nucleic Acids Res. 2003 Feb 15;31(4):1208-15 PMID: 12582240
  4. Inhibition of human papilloma virus E2 DNA binding protein by covalently linked polyamides.
    Nucleic Acids Res. 2003 Feb 15;31(4):1282-91 PMID: 12582248
  5. Design of triple helix forming C-glycoside molecules.
    J Am Chem Soc. 2003 Feb 26;125(8):2084-93 PMID: 12590536
  6. Scanning the human genome with combinatorial transcription factor libraries.
    Nat Biotechnol. 2003 Mar;21(3):269-74 PMID: 12592412
  7. Human zinc fingers as building blocks in the construction of artificial transcription factors.
    Nat Biotechnol. 2003 Mar;21(3):275-80 PMID: 12592413
  8. Targeted regulation of imprinted genes by synthetic zinc-finger transcription factors.
    Gene Ther. 2003 Mar;10(6):513-22 PMID: 12621455
  9. Site-specific mutagenesis by triple helix-forming oligonucleotides containing a reactive nucleoside analog.
    Nucleic Acids Res. 2003 Mar 15;31(6):e31 PMID: 12626730
  10. Cell cycle modulation of gene targeting by a triple helix-forming oligonucleotide.
    J Biol Chem. 2003 Mar 28;278(13):11072-7 PMID: 12538585
  11. Controlling the intracellular localization of fluorescent polyamide analogues in cultured cells.
    Bioorg Med Chem Lett. 2003 May 5;13(9):1565-70 PMID: 12699756
  12. A bis-alkylating triplex forming oligonucleotide inhibits intracellular reporter gene expression and prevents triplex unwinding due to helicase activity.
    Biochemistry. 2003 May 6;42(17):5013-24 PMID: 12718544
  13. Triplex-forming oligodeoxynucleotides targeting survivin inhibit proliferation and induce apoptosis of human lung carcinoma cells.
    Cancer Gene Ther. 2003 May;10(5):403-10 PMID: 12719710
  14. Chimeric nucleases stimulate gene targeting in human cells.
    Science. 2003 May 2;300(5620):763 PMID: 12730593
  15. Enhancing gene targeting with designed zinc finger nucleases.
    Science. 2003 May 2;300(5620):764 PMID: 12730594
  16. Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition.
    J Am Chem Soc. 2003 May 14;125(19):5707-16 PMID: 12733909
  17. Alternative heterocycles for DNA recognition: the benzimidazole/imidazole pair.
    Chemistry. 2003 May 9;9(9):2110-22 PMID: 12740860
  18. Recognition of the DNA minor groove by pyrrole-imidazole polyamides.
    Curr Opin Struct Biol. 2003 Jun;13(3):284-99 PMID: 12831879
  19. Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded.
    Nucleic Acids Res. 1979 Jul 11;6(9):3073-91 PMID: 40208
  20. Oligonucleotide inhibition of IL2R alpha mRNA transcription by promoter region collinear triplex formation in lymphocytes.
    Nucleic Acids Res. 1991 Jun 25;19(12):3435-41 PMID: 2062658
  21. Evidence that a triplex-forming oligodeoxyribonucleotide binds to the c-myc promoter in HeLa cells, thereby reducing c-myc mRNA levels.
    Proc Natl Acad Sci U S A. 1991 Sep 15;88(18):8227-31 PMID: 1896473
  22. Specific inhibition of transcription by triple helix-forming oligonucleotides.
    Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):504-8 PMID: 1731320
  23. A triple helix-forming oligonucleotide-intercalator conjugate acts as a transcriptional repressor via inhibition of NF kappa B binding to interleukin-2 receptor alpha-regulatory sequence.
    J Biol Chem. 1992 Feb 15;267(5):3389-95 PMID: 1737792
  24. Independent modes of transcriptional activation by the p50 and p65 subunits of NF-kappa B.
    Genes Dev. 1992 May;6(5):775-87 PMID: 1577272
  25. Structure of a G.T.A triplet in an intramolecular DNA triplex.
    Biochemistry. 1992 May 26;31(20):4838-46 PMID: 1591244
  26. Oligo(2'-O-methyl)ribonucleotides. Effective probes for duplex DNA.
    FEBS Lett. 1992 May 11;302(2):155-8 PMID: 1633847
  27. Specific recognition of CG base pairs by 2-deoxynebularine within the purine.purine.pyrimidine triple-helix motif.
    Biochemistry. 1993 Mar 9;32(9):2177-85 PMID: 8443159
  28. DNA unwinding upon strand-displacement binding of a thymine-substituted polyamide to double-stranded DNA.
    Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1667-70 PMID: 8383322
  29. Stable triple helices are formed upon binding of RNA oligonucleotides and their 2'-O-methyl derivatives to double-helical DNA.
    C R Acad Sci III. 1992;315(13):521-5 PMID: 1300234
  30. Targeted mutagenesis of DNA using triple helix-forming oligonucleotides linked to psoralen.
    Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7879-83 PMID: 8356097
  31. Targeted mutagenesis of simian virus 40 DNA mediated by a triple helix-forming oligonucleotide.
    J Virol. 1993 Dec;67(12):7324-31 PMID: 8230456
  32. Relative specificities in binding of Watson-Crick base pairs by third strand residues in a DNA pyrimidine triplex motif.
    Nucleic Acids Res. 1993 Sep 25;21(19):4511-5 PMID: 8233785
  33. Peptide nucleic acid.DNA strand displacement loops as artificial transcription promoters.
    Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3892-5 PMID: 8171008
  34. Krüppel-associated boxes are potent transcriptional repression domains.
    Proc Natl Acad Sci U S A. 1994 May 10;91(10):4509-13 PMID: 8183939
  35. Reversible inhibition of gene expression by a psoralen functionalized triple helix forming oligonucleotide in intact cells.
    J Biol Chem. 1994 Jun 17;269(24):16933-7 PMID: 8207016
  36. Triplex formation by the human Ha-ras promoter inhibits Sp1 binding and in vitro transcription.
    J Biol Chem. 1994 Jul 8;269(27):18232-8 PMID: 8027084
  37. Transcription inhibition induced by modified triple helix-forming oligonucleotides: a quantitative assay for evaluation in cells.
    J Mol Biol. 2001 Feb 9;306(1):15-24 PMID: 11178890
  38. Design of polyzinc finger peptides with structured linkers.
    Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1432-6 PMID: 11171968
  39. Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units.
    Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1437-41 PMID: 11171969
  40. Regulation of an endogenous locus using a panel of designed zinc finger proteins targeted to accessible chromatin regions. Activation of vascular endothelial growth factor A.
    J Biol Chem. 2001 Apr 6;276(14):11323-34 PMID: 11145970
  41. Recent developments in sequence selective minor groove DNA effectors.
    Curr Med Chem. 2001 Apr;8(5):475-508 PMID: 11281837
  42. Sequence recognition of DNA by lexitropsins.
    Curr Med Chem. 2001 Apr;8(5):509-16 PMID: 11281838
  43. DNA minor groove alkylating agents.
    Curr Med Chem. 2001 Apr;8(5):533-44 PMID: 11281840
  44. Targeting double stranded DNA with peptide nucleic acid (PNA).
    Curr Med Chem. 2001 Apr;8(5):545-50 PMID: 11281841
  45. The nuclear pore complex as a transport machine.
    J Biol Chem. 2001 May 18;276(20):16593-6 PMID: 11283009
  46. Triplex-induced recombination in human cell-free extracts. Dependence on XPA and HsRad51.
    J Biol Chem. 2001 May 25;276(21):18018-23 PMID: 11278954
  47. 2'-O,4'-C-methylene bridged nucleic acid modification promotes pyrimidine motif triplex DNA formation at physiological pH: thermodynamic and kinetic studies.
    J Biol Chem. 2001 Jan 26;276(4):2354-60 PMID: 11035027
  48. Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides.
    J Mol Biol. 2001 Jun 8;309(3):615-29 PMID: 11397084
  49. Towards a minimal motif for artificial transcriptional activators.
    Chem Biol. 2001 Jun;8(6):583-92 PMID: 11410377
  50. A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter.
    Nat Biotechnol. 2001 Jul;19(7):656-60 PMID: 11433278
  51. Manipulating the mammalian genome by homologous recombination.
    Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8403-10 PMID: 11459982
  52. Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors.
    J Biol Chem. 2001 Aug 3;276(31):29466-78 PMID: 11340073
  53. Triplex-forming molecules: from concepts to applications.
    J Gene Med. 2001 Jul-Aug;3(4):299-310 PMID: 11529659
  54. Regulation of the MDR1 gene by transcriptional repressors selected using peptide combinatorial libraries.
    Mol Pharmacol. 2000 Jul;58(1):1-10 PMID: 10860921
  55. Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers.
    Structure. 2000 Jul 15;8(7):739-50 PMID: 10903945
  56. Stable triple helices formed by oligonucleotide N3'-->P5' phosphoramidates inhibit transcription elongation.
    Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):4365-9 PMID: 8633072
  57. Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair.
    Science. 1996 Feb 9;271(5250):802-5 PMID: 8628995
  58. Positively charged oligonucleotides overcome potassium-mediated inhibition of triplex DNA formation.
    Nucleic Acids Res. 1996 Jun 1;24(11):2143-9 PMID: 8668547
  59. DNA triplex formation selectively inhibits granulocyte-macrophage colony-stimulating factor gene expression in human T cells.
    J Biol Chem. 1996 Jun 14;271(24):14438-44 PMID: 8662666
  60. Recognition of DNA by designed ligands at subnanomolar concentrations.
    Nature. 1996 Aug 8;382(6591):559-61 PMID: 8700233
  61. Efficient inhibition of transcription elongation in vitro by oligonucleotide phosphoramidates targeted to proviral HIV DNA.
    J Mol Biol. 1996 Aug 23;261(3):386-98 PMID: 8780781
  62. Splase: a new class IIS zinc-finger restriction endonuclease with specificity for Sp1 binding sites.
    J Protein Chem. 1996 Jul;15(5):481-9 PMID: 8895094
  63. A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA.
    Nat Struct Biol. 1996 Nov;3(11):940-5 PMID: 8901872
  64. Triple helix-forming oligodeoxyribonucleotides targeted to the human tumor necrosis factor (TNF) gene inhibit TNF production and block the TNF-dependent growth of human glioblastoma tumor cells.
    Cancer Res. 1996 Nov 15;56(22):5156-64 PMID: 8912851
  65. Recombination induced by triple-helix-targeted DNA damage in mammalian cells.
    Mol Cell Biol. 1996 Dec;16(12):6820-8 PMID: 8943337
  66. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites.
    Science. 1997 Jan 31;275(5300):657-61 PMID: 9005850
  67. In vivo persistence of DNA triple helices containing psoralen-conjugated oligodeoxyribonucleotides.
    Nucleic Acids Res. 1996 Dec 15;24(24):4924-32 PMID: 9016662
  68. Potential triple helix-mediated inhibition of IGF-I gene expression significantly reduces tumorigenicity of glioblastoma in an animal model.
    Cancer Gene Ther. 1997 Mar-Apr;4(2):105-12 PMID: 9080119
  69. Design of TATA box-binding protein/zinc finger fusions for targeted regulation of gene expression.
    Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3616-20 PMID: 9108026
  70. A complex containing N-CoR, mSin3 and histone deacetylase mediates transcriptional repression.
    Nature. 1997 May 1;387(6628):43-8 PMID: 9139820
  71. Regulation of gene expression by small molecules.
    Nature. 1997 May 8;387(6629):202-5 PMID: 9144294
  72. Antiparallel polypurine phosphorothioate oligonucleotides form stable triplexes with the rat alpha1(I) collagen gene promoter and inhibit transcription in cultured rat fibroblasts.
    Nucleic Acids Res. 1997 Jun 1;25(11):2182-8 PMID: 9153319
  73. High-frequency intrachromosomal gene conversion induced by triplex-forming oligonucleotides microinjected into mouse cells.
    Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9003-8 PMID: 10900269
  74. Targeting the ets binding site of the HER2/neu promoter with pyrrole-imidazole polyamides.
    J Biol Chem. 2000 Aug 11;275(32):24246-54 PMID: 10818092
  75. Designed sequence-specific minor groove ligands.
    Annu Rev Biophys Biomol Struct. 2000;29:439-61 PMID: 10940255
  76. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.
    Nucleic Acids Res. 2000 Sep 1;28(17):3361-9 PMID: 10954606
  77. Advances in zinc finger engineering.
    Curr Opin Struct Biol. 2000 Aug;10(4):411-6 PMID: 10981627
  78. Chemically regulated zinc finger transcription factors.
    J Biol Chem. 2000 Oct 20;275(42):32617-27 PMID: 10924515
  79. Specific mutations induced by triplex-forming oligonucleotides in mice.
    Science. 2000 Oct 20;290(5491):530-3 PMID: 11039937
  80. Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains.
    J Mol Biol. 2000 Nov 3;303(4):489-502 PMID: 11054286
  81. Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene.
    J Biol Chem. 2000 Oct 27;275(43):33850-60 PMID: 10913152
  82. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases.
    Mol Cell Biol. 2001 Jan;21(1):289-97 PMID: 11113203
  83. In vivo expression of single-stranded DNA in mammalian cells with DNA enzyme sequences targeted to C-raf.
    Antisense Nucleic Acid Drug Dev. 2000 Dec;10(6):415-22 PMID: 11198925
  84. Suppression of insulin-like growth factor type I receptor by a triple-helix strategy inhibits IGF-I transcription and tumorigenic potential of rat C6 glioblastoma cells.
    Proc Natl Acad Sci U S A. 1997 May 27;94(11):5854-9 PMID: 9159164
  85. Transcriptional repression by zinc finger peptides. Exploring the potential for applications in gene therapy.
    J Biol Chem. 1997 Nov 21;272(47):29795-800 PMID: 9368051
  86. Selection of peptides that functionally replace a zinc finger in the Sp1 transcription factor by using a yeast combinatorial library.
    Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):14120-5 PMID: 9391163
  87. Recombination-dependent deletion formation in mammalian cells deficient in the nucleotide excision repair gene ERCC1.
    Proc Natl Acad Sci U S A. 1997 Nov 25;94(24):13122-7 PMID: 9371810
  88. Recognition of GC base pairs by triplex forming oligonucleotides containing nucleosides derived from 2-aminopyridine.
    Nucleic Acids Res. 1997 Dec 15;25(24):4891-8 PMID: 9396793
  89. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands.
    Nature. 1998 Jan 29;391(6666):468-71 PMID: 9461213
  90. Structure-based design of a dimeric zinc finger protein.
    Biochemistry. 1998 Jan 27;37(4):965-70 PMID: 9467467
  91. Triplex-directed modification of genes and gene activity.
    Trends Biochem Sci. 1998 Jan;23(1):4-9 PMID: 9478127
  92. Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants.
    Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):2812-7 PMID: 9501172
  93. Artificial nine zinc-finger peptide with 30 base pair binding sites.
    Biochemistry. 1998 Sep 29;37(39):13827-34 PMID: 9753472
  94. Targeted gene knockout mediated by triple helix forming oligonucleotides.
    Nat Genet. 1998 Oct;20(2):212-4 PMID: 9771719
  95. Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands.
    Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12890-5 PMID: 9789010
  96. Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks.
    Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14628-33 PMID: 9843940
  97. A detailed study of the substrate specificity of a chimeric restriction enzyme.
    Nucleic Acids Res. 1999 Jan 15;27(2):674-81 PMID: 9862996
  98. Dual recognition of double-stranded DNA by 2'-aminoethoxy-modified oligonucleotides: the solution structure of an intramolecular triplex obtained by NMR spectroscopy.
    Biochemistry. 1998 Dec 22;37(51):17714-25 PMID: 9922137
  99. Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code.
    J Mol Biol. 1999 Feb 5;285(5):1917-34 PMID: 9925775
  100. Chromosomal mutations induced by triplex-forming oligonucleotides in mammalian cells.
    Nucleic Acids Res. 1999 Feb 15;27(4):1176-81 PMID: 9927753
  101. Molecular recognition of DNA by small molecules.
    Bioorg Med Chem. 2001 Sep;9(9):2215-35 PMID: 11553460
  102. Alpha-oligonucleotides with anionic phosphodiester and cationic phosphoramidate linkages enhanced stability of DNA triple helix.
    Nucleosides Nucleotides Nucleic Acids. 2001 Apr-Jul;20(4-7):797-9 PMID: 11563118
  103. Chromosome targeting at short polypurine sites by cationic triplex-forming oligonucleotides.
    J Biol Chem. 2001 Oct 19;276(42):38536-41 PMID: 11504712
  104. Proton exchange and local stability in a DNA triple helix containing a G.TA triad.
    Nucleic Acids Res. 2001 Oct 15;29(20):4231-7 PMID: 11600712
  105. Triplex forming oligonucleotides: sequence-specific tools for gene targeting.
    Hum Mol Genet. 2001 Oct 1;10(20):2243-51 PMID: 11673407
  106. Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster.
    Mol Cell. 2000 Nov;6(5):1013-24 PMID: 11106741
  107. PPARgamma knockdown by engineered transcription factors: exogenous PPARgamma2 but not PPARgamma1 reactivates adipogenesis.
    Genes Dev. 2002 Jan 1;16(1):27-32 PMID: 11782442
  108. Design and selection of novel Cys2His2 zinc finger proteins.
    Annu Rev Biochem. 2001;70:313-40 PMID: 11395410
  109. Intracellular generation of single-stranded DNA for chromosomal triplex formation and induced recombination.
    Nucleic Acids Res. 2001 Dec 15;29(24):5140-7 PMID: 11812847
  110. Engineering polydactyl zinc-finger transcription factors.
    Nat Biotechnol. 2002 Feb;20(2):135-41 PMID: 11821858
  111. Custom DNA-binding proteins come of age: polydactyl zinc-finger proteins.
    Curr Opin Biotechnol. 2001 Dec;12(6):632-7 PMID: 11849947
  112. Triplex-forming oligonucleotides: principles and applications.
    Q Rev Biophys. 2002 Feb;35(1):89-107 PMID: 11997982
  113. Sequence-specific gene cleavage in intact mammalian cells by 125I-labeled triplex-forming oligonucleotides conjugated with nuclear localization signal peptide.
    Antisense Nucleic Acid Drug Dev. 2002 Feb;12(1):43-9 PMID: 12022689
  114. Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table.
    Biochemistry. 2002 Jun 4;41(22):7074-81 PMID: 12033941
  115. Recognition of ten base pairs of DNA by head-to-head hairpin dimers.
    J Am Chem Soc. 2002 Jun 19;124(24):6872-8 PMID: 12059208
  116. Regulation of endogenous gene expression with a small-molecule dimerizer.
    Nat Biotechnol. 2002 Jul;20(7):729-33 PMID: 12089560
  117. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases.
    Genetics. 2002 Jul;161(3):1169-75 PMID: 12136019
  118. Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
    Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2758-63 PMID: 10077584
  119. Triple-helix formation of DNA oligomers with methylthiourea-linked nucleosides (DNmt): a kinetic and thermodynamic analysis.
    Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4384-9 PMID: 10200271
  120. Targeted correction of an episomal gene in mammalian cells by a short DNA fragment tethered to a triplex-forming oligonucleotide.
    J Biol Chem. 1999 Apr 23;274(17):11541-8 PMID: 10206960
  121. Peptide nucleic acid (PNA) binding-mediated induction of human gamma-globin gene expression.
    Nucleic Acids Res. 1999 Jul 1;27(13):2806-13 PMID: 10373600
  122. Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences.
    Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9568-73 PMID: 10449733
  123. Chimeric restriction enzymes: what is next?
    Biol Chem. 1999 Jul-Aug;380(7-8):841-8 PMID: 10494832
  124. Gene activation by triplex-forming oligonucleotide coupled to the activating domain of protein VP16.
    Nucleic Acids Res. 1999 Oct 15;27(20):3995-4000 PMID: 10497263
  125. Inhibition of gene expression by triple helix formation in hepatoma cells.
    J Biol Chem. 1995 Nov 24;270(47):28402-7 PMID: 7499344
  126. Search for the optimal linker in tandem hairpin polyamides.
    Bioorg Med Chem. 2002 Oct;10(10):3339-49 PMID: 12150881
  127. Pharmacological regulation of protein expression from adeno-associated viral vectors in the eye.
    Mol Ther. 2002 Aug;6(2):238-42 PMID: 12161190
  128. Cellular import mediated by nuclear localization signal Peptide sequences.
    Chem Biol. 2002 Aug;9(8):943-8 PMID: 12204694
  129. Specific inhibition of ICAM-1 expression mediated by gene targeting with Triplex-forming oligonucleotides.
    J Biol Chem. 2002 Sep 6;277(36):32473-9 PMID: 12080053
  130. Design of artificial transcriptional activators with rigid poly-L-proline linkers.
    J Am Chem Soc. 2002 Nov 6;124(44):13067-71 PMID: 12405833
  131. Cell-free and cellular activities of a DNA sequence selective hairpin polyamide-CBI conjugate.
    J Biol Chem. 2002 Nov 8;277(45):42431-7 PMID: 12196541
  132. Targeted derepression of the human immunodeficiency virus type 1 long terminal repeat by pyrrole-imidazole polyamides.
    J Virol. 2002 Dec;76(23):12349-54 PMID: 12414976
  133. Induction of angiogenesis in a mouse model using engineered transcription factors.
    Nat Med. 2002 Dec;8(12):1427-32 PMID: 12415262
  134. The use of synthetic oligonucleotides as protein inhibitors and anticode drugs in cancer therapy: accomplishments and limitations.
    Curr Cancer Drug Targets. 2002 Dec;2(4):355-68 PMID: 12470211
  135. Transcription dependence of chromosomal gene targeting by triplex-forming oligonucleotides.
    J Biol Chem. 2003 Jan 31;278(5):3357-62 PMID: 12431993
  136. Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands.
    J Mol Biol. 2003 Feb 14;326(2):371-80 PMID: 12559907
  137. Selective inhibition of transcription of the Ets2 gene in prostate cancer cells by a triplex-forming oligonucleotide.
    Nucleic Acids Res. 2003 Feb 1;31(3):833-43 PMID: 12560478
  138. Design of artificial transcription factors to selectively regulate the pro-apoptotic bax gene.
    Nucleic Acids Res. 2003 Feb 1;31(3):e10 PMID: 12560513
  139. Molecular design of a pyrrole-imidazole hairpin polyamides for effective DNA alkylation.
    Chemistry. 2002 Oct 18;8(20):4781-90 PMID: 12561118
  140. In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence.
    Nature. 1994 Dec 15;372(6507):642-5 PMID: 7990954
  141. DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.
    Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12357-61 PMID: 7809040
  142. Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation.
    Mol Cell Biol. 1995 Mar;15(3):1759-68 PMID: 7862165
  143. An assessment of the antisense properties of RNase H-competent and steric-blocking oligomers.
    Nucleic Acids Res. 1995 Apr 11;23(7):1197-203 PMID: 7537874
  144. Pax5 (BSAP) regulates the murine immunoglobulin 3' alpha enhancer by suppressing binding of NF-alpha P, a protein that controls heavy chain transcription.
    Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5336-40 PMID: 7777508
  145. Inhibition of in vitro transcription by a triplex-forming oligonucleotide targeted to human c-myc P2 promoter.
    Biochemistry. 1995 Jun 27;34(25):8165-71 PMID: 7794930
  146. A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine.
    Proc Natl Acad Sci U S A. 1995 Aug 1;92(16):7297-301 PMID: 7638184
  147. Inhibition of aromatase expression by a psoralen-linked triplex-forming oligonucleotide targeted to a coding sequence.
    FEBS Lett. 1995 Sep 25;372(2-3):222-8 PMID: 7556673
  148. Triple helix directed psoralen adducts induce a low frequency of recombination in an SV40 shuttle vector.
    Biochim Biophys Acta. 1995 Sep 19;1263(3):235-40 PMID: 7548210
  149. Suppression of c-myc oncogene expression by a polyamine-complexed triplex forming oligonucleotide in MCF-7 breast cancer cells.
    Nucleic Acids Res. 1995 Sep 11;23(17):3594-9 PMID: 7567474
  150. Temporary ex vivo inhibition of the expression of the human oncogene HER2 (NEU) by a triple helix-forming oligonucleotide.
    Cancer Res. 1996 Feb 1;56(3):515-22 PMID: 8564964
  151. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain.
    Proc Natl Acad Sci U S A. 1996 Feb 6;93(3):1156-60 PMID: 8577732
  152. Triplex formation by a psoralen-conjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine.
    Nucleic Acids Res. 1996 Feb 15;24(4):730-6 PMID: 8604317
  153. Sequence specificity of triplex DNA formation: Analysis by a combinatorial approach, restriction endonuclease protection selection and amplification.
    Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2811-6 PMID: 8610123
  154. Poly(pyrimidine) . poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH.
    Nucleic Acids Res. 1984 Aug 24;12(16):6603-14 PMID: 6473110
  155. Effect of insertions, deletions, and double-strand breaks on homologous recombination in mouse L cells.
    Mol Cell Biol. 1985 Apr;5(4):684-91 PMID: 3990689
  156. Topological requirements for homologous recombination among DNA molecules transfected into mammalian cells.
    Mol Cell Biol. 1985 Aug;5(8):2080-9 PMID: 3018550
  157. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[alpha]-thymidylate covalently linked to an azidoproflavine derivative.
    Nucleic Acids Res. 1987 Oct 12;15(19):7749-60 PMID: 3671065
  158. Sequence-specific cleavage of double helical DNA by triple helix formation.
    Science. 1987 Oct 30;238(4827):645-50 PMID: 3118463
  159. Lexitropsins: rational design of DNA sequence reading agents as novel anti-cancer agents and potential cellular probes.
    Anticancer Drug Des. 1988 Jun;3(1):25-40 PMID: 2838035
  160. Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro.
    Science. 1988 Jul 22;241(4864):456-9 PMID: 3293213
  161. GAL4-VP16 is an unusually potent transcriptional activator.
    Nature. 1988 Oct 6;335(6190):563-4 PMID: 3047590
  162. Specificity in formation of triple-stranded nucleic acid helical complexes: studies with agarose-linked polyribonucleotide affinity columns.
    Biochemistry. 1988 Dec 27;27(26):9108-12 PMID: 3242616
  163. Protein encoded by v-erbA functions as a thyroid-hormone receptor antagonist.
    Nature. 1989 Jun 22;339(6226):593-7 PMID: 2733791
  164. Recognition of thymine adenine.base pairs by guanine in a pyrimidine triple helix motif.
    Science. 1989 Sep 1;245(4921):967-71 PMID: 2549639
  165. Transport of oligonucleotides across natural and model membranes.
    Biochim Biophys Acta. 1994 Jun 29;1197(2):95-108 PMID: 8031827
  166. In vivo generation of highly abundant sequence-specific oligonucleotides for antisense and triplex gene regulation.
    Nucleic Acids Res. 1994 Jul 25;22(14):2830-6 PMID: 8052538
  167. Differential regulation of gene expression in vivo by triple helix-forming oligonucleotides as detected by a reporter enzyme.
    Antisense Res Dev. 1994 Spring;4(1):1-8 PMID: 8061512
  168. Binding of T and T analogs to CG base pairs in antiparallel triplexes.
    Nucleic Acids Res. 1994 Aug 11;22(15):3233-40 PMID: 8065940
  169. Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage.
    Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11163-7 PMID: 7972027
  170. Targeting topoisomerase I cleavage to specific sequences of DNA by triple helix-forming oligonucleotide conjugates. A comparison between a rebeccamycin derivative and camptothecin.
    C R Acad Sci III. 1999 Sep;322(9):785-90 PMID: 10547719
  171. Transcription of the human c-Src promoter is dependent on Sp1, a novel pyrimidine binding factor SPy, and can be inhibited by triplex-forming oligonucleotides.
    J Biol Chem. 2000 Jan 14;275(2):847-54 PMID: 10625617
  172. Triple-helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway.
    Mol Cell Biol. 2000 Feb;20(3):990-1000 PMID: 10629056
  173. Selective inhibition of monocyte chemoattractant protein-1 gene expression in human embryonal kidney cells by specific triple helix-forming oligonucleotides.
    J Immunol. 2000 Feb 15;164(4):2070-6 PMID: 10657660
  174. Regulated gene expression systems.
    Gene Ther. 2000 Jan;7(2):120-5 PMID: 10673717
  175. Positive and negative regulation of endogenous genes by designed transcription factors.
    Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1495-500 PMID: 10660690
  176. Zinc finger proteins as designer transcription factors.
    J Biol Chem. 2000 Mar 24;275(12):8742-8 PMID: 10722717
  177. Unambiguous demonstration of triple-helix-directed gene modification.
    Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3084-8 PMID: 10716704
  178. Pyrimidine morpholino oligonucleotides form a stable triple helix in the absence of magnesium ions.
    Biochem Biophys Res Commun. 2000 Apr 13;270(2):363-9 PMID: 10753631
  179. Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides.
    Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3862-7 PMID: 10760257
  180. Activation of gene expression by small molecule transcription factors.
    Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3930-5 PMID: 10760265
  181. Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future.
    FASEB J. 2000 Jun;14(9):1041-60 PMID: 10834926
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkg815
Published
2003-11-01
Pages
6064-78
Language
English
Region
England
NLM ID
0411011
PMCID
PMC275457
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkg815 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2